Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules

2018 ◽  
Vol 59 (1) ◽  
pp. 236-244 ◽  
Author(s):  
Callum J. Dickson ◽  
Viktor Hornak ◽  
Dallas Bednarczyk ◽  
Jose S. Duca
Keyword(s):  
Membrane Partitioning

Alcohol enhanced permeation in model membranes. Part II. Thermodynamic analysis of membrane partitioning

2011 ◽  
Vol 420 (2) ◽  
pp. 216-222 ◽  
Author(s):  
Gabriela Oliveira ◽  
Anthony E. Beezer ◽  
Jonathan Hadgraft ◽  
Majella E. Lane
Keyword(s):  
Thermodynamic Analysis ◽  
Model Membranes ◽  
Membrane Partitioning

scholarly journals Molecular simulations of lipid membrane partitioning and translocation by bacterial quorum sensing modulators

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246187
Author(s):  
Tianyi Jin ◽  
Samarthaben J. Patel ◽  
Reid C. Van Lehn
Keyword(s):  
Quorum Sensing ◽  
Lipid Bilayers ◽  
Lipid Membrane ◽  
Computational Cost ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Communication Process ◽  
Free Energies ◽  
Membrane Partitioning ◽  
Solvent Model

Quorum sensing (QS) is a bacterial communication process mediated by both native and non-native small-molecule quorum sensing modulators (QSMs), many of which have been synthesized to disrupt QS pathways. While structure-activity relationships have been developed to relate QSM structure to the activation or inhibition of QS receptors, less is known about the transport mechanisms that enable QSMs to cross the lipid membrane and access intracellular receptors. In this study, we used atomistic MD simulations and an implicit solvent model, called COSMOmic, to analyze the partitioning and translocation of QSMs across lipid bilayers. We performed umbrella sampling at atomistic resolution to calculate partitioning and translocation free energies for a set of naturally occurring QSMs, then used COSMOmic to screen the water-membrane partition and translocation free energies for 50 native and non-native QSMs that target LasR, one of the LuxR family of quorum-sensing receptors. This screening procedure revealed the influence of systematic changes to head and tail group structures on membrane partitioning and translocation free energies at a significantly reduced computational cost compared to atomistic MD simulations. Comparisons with previously determined QSM activities suggest that QSMs that are least likely to partition into the bilayer are also less active. This work thus demonstrates the ability of the computational protocol to interrogate QSM-bilayer interactions which may help guide the design of new QSMs with engineered membrane interactions.

scholarly journals Design of Soluble Transmembrane Helix for Measurement of Water-Membrane Partitioning

2009 ◽  
Vol 96 (3) ◽  
pp. 336a
Author(s):  
Yoshiaki Yano ◽  
Norie Shimai ◽  
Katsumi Matsuzaki
Keyword(s):  
Transmembrane Helix ◽  
Membrane Partitioning

scholarly journals Retraction for Sorek et al., “Activation Status-Coupled Transient S Acylation Determines Membrane Partitioning of a Plant Rho-Related GTPase”

2017 ◽  
Vol 37 (16) ◽  
Author(s):  
Nadav Sorek ◽  
Limor Poraty ◽  
Hasana Sternberg ◽  
Einat Bar ◽  
Efraim Lewinsohn ◽  
...  
Keyword(s):  
Membrane Partitioning ◽  
Activation Status

Effects of glycerol and urea on micellization, membrane partitioning and solubilization by a non-ionic surfactant

2010 ◽  
Vol 150 (1-3) ◽  
pp. 119-128 ◽  
Author(s):  
Hiren Patel ◽  
Gaurav Raval ◽  
Mozhgan Nazari ◽  
Heiko Heerklotz
Keyword(s):  
Ionic Surfactant ◽  
Membrane Partitioning

Correlation between Membrane Partitioning and Functional Activity in a Single Lipid Vesicle Assay Establishes Design Guidelines for Antiviral Peptides

Small ◽  
2015 ◽  
Vol 11 (20) ◽  
pp. 2372-2379 ◽  
Author(s):  
Joshua A. Jackman ◽  
Rathi Saravanan ◽  
Yibang Zhang ◽  
Seyed R. Tabaei ◽  
Nam-Joon Cho
Keyword(s):  
Functional Activity ◽  
Design Guidelines ◽  
Lipid Vesicle ◽  
Membrane Partitioning ◽  
Antiviral Peptides
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